Assembly of a complete genome sequence for Gemmata obscuriglobus reveals a novel prokaryotic rRNA operon gene architecture

Josef D. Franke, Wilson R. Blomberg, Robert T. Todd, Robert W. Thomas, Anna M. Selmecki

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Gemmata obscuriglobus is a Gram-negative bacterium with several intriguing biological features. Here, we present a complete, de novo whole genome assembly for G. obscuriglobus which consists of a single, circular 9 Mb chromosome, with no plasmids detected. The genome was annotated using the NCBI Prokaryotic Genome Annotation pipeline to generate common gene annotations. Analysis of the rRNA genes revealed three interesting features for a bacterium. First, linked G. obscuriglobus rrn operons have a unique gene order, 23S–5S–16S, compared to typical prokaryotic rrn operons (16S–23S–5S). Second, G. obscuriglobus rrn operons can either be linked or unlinked (a 16S gene is in a separate genomic location from a 23S and 5S gene pair). Third, all of the 23S genes (5 in total) have unique polymorphisms. Genome analysis of a different Gemmata species (SH-PL17), revealed a similar 23S–5S–16S gene order in all of its linked rrn operons and the presence of an unlinked operon. Together, our findings show that unique and rare features in Gemmata rrn operons among prokaryotes provide a means to better define the evolutionary relatedness of Gemmata species and the divergence time for different Gemmata species. Additionally, these rrn operon differences provide important insights into the rrn operon architecture of common ancestors of the planctomycetes.

Original languageEnglish (US)
Pages (from-to)2095-2105
Number of pages11
JournalAntonie van Leeuwenhoek, International Journal of General and Molecular Microbiology
Volume111
Issue number11
DOIs
StatePublished - Nov 1 2018

Bibliographical note

Funding Information:
Funding This work is supported by a Nebraska LB692 Tobacco Settlement Biomedical Research Development Award and a Nebraska Established Program to Stimulate Competitive Research (EPSCoR) First Award to A.M.S., a Creighton University Ferlic Summer Undergraduate Research

Funding Information:
Fellowship to W.R.B., and a Creighton University CURAS Faculty Research Fund Award to J.D.F.

Funding Information:
We would like to thank Drs. Jill Blankenship and Chuck Deutch for comments on the manuscript and Curtis Focht for assistance with bioinformatic programming. Data deposition: NCBI BioProject ID: PRJNA429867, CP025958. SRA accession for PacBio and Illumina data is SRP132554. None of the authors have any competing financial conflicts of interests.

Publisher Copyright:
© 2018, Springer International Publishing AG, part of Springer Nature.

Copyright:
Copyright 2018 Elsevier B.V., All rights reserved.

Keywords

  • De novo genome assembly
  • PVC superphylum
  • Phylogenetics
  • Planctomycete
  • rrn operon

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